The North Sea's largest colony of puffins has suffered a sudden collapse in numbers, raising fears that climate change and overfishing may be destroying the sea bird's food supplies.

Naturalists working on the Isle of May, a major seabird colony on the Firth of Forth near Edinburgh, disclosed today that puffin numbers on the island have unexpectedly fallen by nearly a third this year after decades of continual increases in population.

Only 70% of nests on the island are now being occupied, while adult birds that have landed on the island have been underweight and malnourished. The finding follows the discovery of numerous dead puffins washing up along the coast over the last two winters.

Professor Mike Harris, the lead researcher with the Oxfordshire-based Centre for Ecology and Hydrology, said the precise causes of the decline were complex and unclear but it seemed very likely that warming seas, changes and shifts in puffin food supplies, and intensive fishing across the North Sea were to blame.

Although the bird – which has a relatively long 30-year lifecycle - congregates in large colonies such as the Isle of May to breed in the spring, it spreads across the sea to winter on the water. It also has a wide and varied diet, from zooplankton and worms, to small fish such as sand eels, and squid.

As a result, its decline suggests a profound problem across the North Sea rather than an isolated or one-off event, said Harris. "We're looking for something acting over a substantial part of the North Sea," he said. "Something big is going on at a wide scale."

Puffins on the Isle of May, a nature reserve owned by Scottish Natural Heritage, had grown markedly from a handful of pairs in the 1950s, to about 69,300 pairs in 2003. But the latest five-yearly survey has estimated the population to be about 41,000 pairs today.

Based on the historic rates of increase, it was expected there could be up to 100,000 pairs in the colony. Yet this year's nest burrow occupancy rate is 70% compared to 100% in past surveys. As a result, Harris's team will carry out another full survey next year to see whether the decline continues.

Marine biologists have already identified a marked shift northwards of warm-water plankton and other indicator species in the North Sea – disrupting the marine food chain. Sand eels – one of the key prey species for larger fish and sea birds such as the puffin – have also declined due to intensive fishing, often to produce feed for salmon farms.

Harris said it was possible this decline was short-lived. New potential food sources were arriving in the North Sea to replace sand eels, although one abundant new species - the snake pipefish – had proven to be too bony and indigestible.

But after 35 years studying the Isle of May colony, he added: "This is the first year I have had any concern about the future. We're not crying doom and despondency yet but we're alerting ourselves to the fact that something is going. We need to find out what it is."

A spokesman for the RSPB, Grahame Madge, said until now seabirds affected by environment changes included the Arctic tern and kittiwakes, which feed in the top few inches of the ocean. "The fact that puffins are similarly in trouble - and we have evidence we're heading for a bad year generally for seabirds - is very troubling.

"The puffin is absolutely expert in obtaining fish and flies better underwater than in the air. That these birds are showing early signs of suffering is something that clearly needs to be addressed."